5XDX

Bovine heart cytochrome c oxidase in the reduced state with pH 7.3 at 1.99 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of bovine cytochrome c oxidase in the ligand-free reduced state at neutral pH.

Luo, F.Shinzawa-Itoh, K.Hagimoto, K.Shimada, A.Shimada, S.Yamashita, E.Yoshikawa, S.Tsukihara, T.

(2018) Acta Crystallogr F Struct Biol Commun 74: 92-98


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 1
A, N
514Bos taurusGene Names: MT-CO1 (COI, COXI, MTCO1)
EC: 1.9.3.1
Find proteins for P00396 (Bos taurus)
Go to Gene View: MT-CO1
Go to UniProtKB:  P00396
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 2
B, O
227Bos taurusGene Names: MT-CO2 (COII, COXII, MTCO2)
Find proteins for P68530 (Bos taurus)
Go to Gene View: MT-CO2
Go to UniProtKB:  P68530
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 3
C, P
260Bos taurusGene Names: MT-CO3 (COIII, COXIII, MTCO3)
Find proteins for P00415 (Bos taurus)
Go to Gene View: MT-CO3
Go to UniProtKB:  P00415
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
D, Q
147Bos taurusGene Names: COX4I1 (COX4)
Find proteins for P00423 (Bos taurus)
Go to Gene View: COX4I1
Go to UniProtKB:  P00423
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 5A, mitochondrial
E, R
109Bos taurusGene Names: COX5A
Find proteins for P00426 (Bos taurus)
Go to Gene View: COX5A
Go to UniProtKB:  P00426
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 5B, mitochondrial
F, S
94Bos taurusGene Names: COX5B
Find proteins for P00428 (Bos taurus)
Go to Gene View: COX5B
Go to UniProtKB:  P00428
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 6A2, mitochondrial
G, T
85Bos taurusGene Names: COX6A2 (COX6A)
Find proteins for P07471 (Bos taurus)
Go to Gene View: COX6A2
Go to UniProtKB:  P07471
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 6B1
H, U
85Bos taurusGene Names: COX6B1 (COX6B)
Find proteins for P00429 (Bos taurus)
Go to Gene View: COX6B1
Go to UniProtKB:  P00429
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide VIc
I, V
73Bos taurusGene Names: COX6C
Find proteins for P04038 (Bos taurus)
Go to Gene View: COX6C
Go to UniProtKB:  P04038
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit VIIa-heart
J, W
59Bos taurusGene Names: COX7A1 (COX7A, COX7AH)
Find proteins for P07470 (Bos taurus)
Go to Gene View: COX7A1
Go to UniProtKB:  P07470
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit VIIb
K, X
56Bos taurusGene Names: COX7B
Find proteins for P13183 (Bos taurus)
Go to Gene View: COX7B
Go to UniProtKB:  P13183
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit VIIc
L, Y
47Bos taurusGene Names: COX7C (COX7CP1)
Find proteins for P00430 (Bos taurus)
Go to Gene View: COX7C
Go to UniProtKB:  P00430
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit VIII-heart
M, Z
46Bos taurusGene Names: COX8B (COX8H)
Find proteins for P10175 (Bos taurus)
Go to UniProtKB:  P10175
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

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A, N
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
ZN
Query on ZN

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F, S
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, C, N, P
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PEK
Query on PEK

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C, G, T
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
PHOSPHATIDYLETHANOLAMINE, 2-ARACHIDONOYL-1-STEAROYL-SN-GLYCEROL-3-PHOSPHOETHANOLAMINE
C43 H78 N O8 P
ANRKEHNWXKCXDB-BHFWLYLHSA-N
 Ligand Interaction
CDL
Query on CDL

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C, G, P, T
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
DMU
Query on DMU

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C, M, P, Z
DECYL-BETA-D-MALTOPYRANOSIDE
DECYLMALTOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
CUA
Query on CUA

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B, O
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B, C, D, E, F, N, P, R, S
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CHD
Query on CHD

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B, C, J, O, P, W
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
 Ligand Interaction
PSC
Query on PSC

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E, O
(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE
PHOSPHATIDYLCHOLINE, 2-LINOLEOYL-1-PALMITOYL-SN-GYCEROL-3-PHOSPHOCHOLINE
C42 H81 N O8 P
JLPULHDHAOZNQI-AUSZDXHESA-O
 Ligand Interaction
MG
Query on MG

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A, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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A, N
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
TGL
Query on TGL

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A, D, L, O, Q, Y
TRISTEAROYLGLYCEROL
TRIACYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
 Ligand Interaction
PGV
Query on PGV

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Download CCD File 
A, C, M, N, P
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
PHOSPHATIDYLGLYCEROL, 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
A, B, N, O
L-PEPTIDE LINKINGC6 H11 N O3 SMET
SAC
Query on SAC
I, V
L-PEPTIDE LINKINGC5 H9 N O4SER
TPO
Query on TPO
G, T
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 183.044α = 90.00
b = 205.691β = 90.00
c = 177.797γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
JSP CRESTJapanJPMJCR12M3

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-21
    Type: Database references